Methane is a potent greenhouse gas emitted from coastal marshes. It is well understood that sea-level rise both affects methane emissions directly and indirectly through shifts in plant community composition. The role of intraspecific genetic variation in explaining variation in plant traits and methane emissions is much less studied. Here, we exposed 26 Schoenoplectus americanus genotypes "resurrected" from up to century-old seedbanks at two Chesapeake Bay marshes to different levels of flooding and salinity and the presence or absence of a competing species, Spartina patens, to investigate the roles of environmental conditions, species composition, and plant traits in driving methane emissions. Comparisons across environmental treatments strongly regulated plant traits and methane emissions. Unexpectedly, genetic variation driven by plant provenance explained more variation in methane emissions than did community composition. These findings add to a growing understanding of the often-underestimated role of genetic variation in regulating ecosystem functioning.